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Yorodumi- PDB-2h6b: Crystal structure of oxidized CprK in complex with o-chlorophenol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h6b | ||||||
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Title | Crystal structure of oxidized CprK in complex with o-chlorophenolacetic acid | ||||||
Components | ChloroPhenol Reduction gene K | ||||||
Keywords | DNA BINDING PROTEIN / halorespiration / DNA binding / chlorinated ligand / chlorophenol / CprK / helix-turn-helix | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfitobacterium hafniense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å | ||||||
Authors | Joyce, M.G. / Levy, C. / Leys, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: CprK Crystal Structures Reveal Mechanism for Transcriptional Control of Halorespiration. Authors: Joyce, M.G. / Levy, C. / Pop, S.M. / Biehl, B.D. / Doukov, T.I. / Ryter, J.M. / Mazon, H. / Smidt, H. / van den Heuvel, R.H. / Ragsdale, S.W. / van der Oost, J. / Leys, D. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN ANY UNIPROT REFERENCE SEQUENCE DATABASE ...SEQUENCE THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN ANY UNIPROT REFERENCE SEQUENCE DATABASE AT THE TIME OF PROCESSING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h6b.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h6b.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 2h6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h6b ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h6b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The second part of the biological assembly is generated by the two fold axis: -x,-y,z |
-Components
#1: Protein | Mass: 28395.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: Q18R04, UniProt: Q8RPJ2*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.8 M Ammonium sulphate, 1mM orthochlorophenol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.9 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 35512 / % possible obs: 99.2 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→19.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.111 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.915 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.258 Å / Total num. of bins used: 20
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